The report was generated using the JSEQ_scRNAseq single-cell analysis pipeline. For more information, please visit: https://github.com/jkubis96/JSEQ_scRNAseq


1 Analysis Configuration Parameters

Parameter Value
mt_per 25
scale_factor 1e+06
n_features 1500
c_res 0.5
heterogeneity var
mt_cssg FALSE
m_val 0.05
top_m 50
max_genes 1000
max_combine 1000
loss_val 0.05
s_factor 0.7
p_bin 0.1
drop TRUE
min_c 10

The parameters above were used during the current analysis.
If you need to apply different analysis conditions, modify the parameters in the configuration file.

Parameters description:

  • mt_per
    Maximum percentage of mitochondrial genes per cell.
    Default: 25%
  • down
    Lower threshold for the number of genes per cell.
    Default: NA (automatically computed if NA)
  • up
    Upper threshold for the number of genes per cell.
    Default: NA (automatically computed if NA)
  • scale_factor
    Scale factor used for data normalization.
  • n_features
    Number of variable features to detect for clustering.
  • c_res
    Clustering resolution — higher values produce more clusters.
  • heterogeneity
    Method for estimating cluster heterogeneity.
    Options: var (within-cluster variance), deg (deregulated gene profiles).
    Default: deg
  • mt_cssg
    Whether to include mitochondrial genes when creating subclasses and subtypes.
    Options: TRUE, FALSE.
    Default: FALSE
  • m_val
    Maximum p-value threshold for marker detection in advanced subtype analyses.
    Default: 0.05
  • top_m
    Maximum number of top markers used for naming clusters based on effect size metrics.
    Default: 50
  • max_genes
    Maximum number of input genes considered in cluster heterogeneity discovery.
    Default: 1000
  • max_combine
    Maximum number of initial combinations for each iteration during heterogeneity discovery.
    Default: 1000
  • loss_val
    Assigned value for potentially unclassified cells within a cluster.
  • s_factor
    Maximum split factor for gene occurrence in heterogeneity discovery (0.2–1).
    Default: 0.8
  • p_bin
    Minimum cell proportion required for population presence based on binomial test p-value.
    Default: 0.05
  • min_c
    Minimum cell proportion required for population presence as defined by the user (independent of binomial test).
    Default: 10
  • drop
    Boolean indicating whether to drop non-significant subtypes based on p_bin and min_c.
    Default: TRUE

The configuration file is available in the directory:
JSEQ_scRNAseq/requirements_file/config_file.conf

Additional configuration files for other analysis steps can also be found in:
JSEQ_scRNAseq/requirements_file

For more information, please visit:
https://github.com/jkubis96/JSEQ_scRNAseq



2 Cell content analysis

2.1 Read distribution across genomic features

2.2 Count (UMI) per barcode (cell)

2.3 Cell barcode knee plot

The above graph illustrates general trends and quality metrics at the initial stage of single-cell analysis; however, it does not represent the final number of detected cells.

2.4 Ratio of number of genes to counts

2.5 Number of genes and counts per cell

2.6 Percentage of ribosomal and mitochondrial genes [%]



3 Quality control of cell content

3.1 Genes per cell content & thresholds

3.2 Genes upper & lower thresholds per cell

3.3 Number of cells across different stages of analysis



4 Gene expression analysis across cells

4.1 Top highly variable genes in the dataset



5 Princilpe component selection

5.1 ElbowPlot - principal components cutoff

5.2 JackStrawPlot - PC significance



6 Cells clustering

6.1 UMAP clusters



7 Subclasses identification based on marker genes

7.1 PCA cisualization of subclasses

7.2 UMAP visualization of subclasses

7.3 Subclasses - cell composition


7.4 Subclasses markers - top 25


Top 25 merkers
genes pct_occurrence esm avg_logFC p_val cluster p_adj_bf p_adj_bh subclass
4930556G01Rik 1.0000000 23.9022539 9.0758183 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Gm18985 0.9090909 19.4858205 9.3266475 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Scn1a 1.0000000 15.4411637 7.8446669 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Rassf6 0.9090909 14.9803329 8.3302664 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Gm33594 0.8181818 14.2863110 9.0676220 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Zfp536.var2 0.9090909 12.6603477 7.7250367 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Col6a4 0.7272727 11.6750888 8.9683165 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Gm29865 0.8181818 10.4756566 7.5963412 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Sugct.var1 0.9090909 9.4800931 6.6899761 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Ido2 0.8181818 9.2158400 7.1815790 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Dgki.var1 0.9090909 8.8739807 6.5749948 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Gm40375 0.7272727 8.4841704 7.1540302 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Slc17a9 0.9090909 8.1299958 6.2600975 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Lipn 0.5454545 8.0562988 8.5338397 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Sorcs1 0.7272727 8.0411011 7.0347095 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Gm20756 0.4545455 7.4214580 9.9622194 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Sh3gl2 0.9090909 6.7189661 5.7612065 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Nfix 1.0000000 6.7182054 5.5549652 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Capn13 0.6363636 6.6828143 6.7673361 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Pde6a 0.7272727 6.6751268 6.2724389 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Rassf2 0.6363636 6.5007340 6.7292426 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Gabra6 0.4545455 6.3123897 7.9380461 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Cnga3 0.3636364 6.0791823 9.6751983 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Wnt2 0.3636364 6.0608144 9.6655899 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Fam71e2 0.4545455 5.7305394 7.2610908 0.0000000 3 0.0000000 0.0000000 CTX Foxg1 4930556g01rik
Gm32067 0.4329897 1.4624655 3.2320719 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Olfr1109 0.2680412 1.2139578 3.7965818 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Rnf19a 0.2577320 1.2121344 3.9703453 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Cux2 0.2371134 1.1630586 4.0620642 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Cdk8 0.4845361 1.1451771 2.3341793 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Trdmt1 0.7525773 1.1326122 1.5858954 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
4931429P17Rik 0.2474227 1.1189843 3.7018578 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Pvr 0.2783505 1.1128852 3.3605800 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Dip2b 0.6288660 1.1067802 1.8467036 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Usp54 0.2886598 1.0937916 3.1370970 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Marchf1 0.3505155 1.0874551 2.7302633 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Cdh13.var1 0.3608247 1.0255035 2.5468172 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Tor3a 0.3814433 1.0120809 2.4285635 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
AW554918 0.2680412 1.0030658 3.0478810 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Scnn1g 0.3711340 1.0019978 2.4250469 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Onecut2 0.4020619 0.9832870 2.2215553 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Gm48228 0.5051546 0.9485065 1.8396507 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Csnk1g1 0.2371134 0.9473673 3.0758585 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
D630023O14Rik 0.1134021 0.9208238 5.6636055 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Fmnl2 0.4432990 0.9207342 1.9597661 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Atp1b2 0.1855670 0.9205405 3.5640036 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Gclc 0.3298969 0.9200055 2.4051085 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Ccdc60 0.2680412 0.9147939 2.6516617 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Aldh1a2 0.1855670 0.9137609 3.5466750 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Gabrd 0.1340206 0.8887066 4.3375463 0.0000000 1 0.0000000 0.0000000 CTX Foxg1 Cdh23.var1
Gm10718 0.7234043 5.3702037 6.9472319 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm10801 0.9148936 5.0866180 4.9421851 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm10722 0.7659574 5.0746500 6.0229419 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm10717 0.5744681 3.8380865 6.3015372 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm10800 0.8936170 3.8273154 4.0969425 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm33838 0.5957447 3.6538981 5.6838918 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm11168 0.3191489 2.5918347 7.4491283 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm10719 0.3617021 2.4969814 5.7171414 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm10721 0.2765957 2.2367176 6.5193877 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm10715 0.0851064 1.0918795 5.7071864 0.0000000 2 0.0000000 0.0000000 CTX Foxg1 Gm10801
Gm10720 0.0851064 0.9613444 4.7774679 0.0000000 2 0.0000002 0.0000000 CTX Foxg1 Gm10801
Rwdd3 0.0638298 0.9299216 5.4278515 0.0000000 2 0.0000030 0.0000002 CTX Foxg1 Gm10801
Ss18 0.0851064 0.7871291 3.7039905 0.0000020 2 0.0004383 0.0000337 CTX Foxg1 Gm10801
Abl2 0.0851064 0.7475406 3.4661175 0.0000082 2 0.0018139 0.0001296 CTX Foxg1 Gm10801
Zfp462 0.1276596 0.6555763 2.4786531 0.0000891 2 0.0197795 0.0011635 CTX Foxg1 Gm10801
Gm45740 0.0638298 0.6364140 3.4835747 0.0000597 2 0.0132469 0.0008731 CTX Foxg1 Gm10801
Ddx50 0.0638298 0.6188590 3.3201446 0.0002451 2 0.0544063 0.0027622 CTX Foxg1 Gm10801
Slc6a6 0.0638298 0.6167544 3.4162328 0.0000629 2 0.0139693 0.0008731 CTX Foxg1 Gm10801
Dnajc1 0.0638298 0.6046450 3.2547652 0.0002377 2 0.0527649 0.0027622 CTX Foxg1 Gm10801
Twf1 0.0638298 0.5731906 2.9640853 0.0016644 2 0.3695076 0.0153961 CTX Foxg1 Gm10801
Fam189a1 0.0638298 0.5548877 3.1123516 0.0002489 2 0.0552448 0.0027622 CTX Foxg1 Gm10801
Runx1t1 0.0638298 0.5376714 2.9328344 0.0007283 2 0.1616819 0.0076991 CTX Foxg1 Gm10801
Litaf 0.0638298 0.5208872 2.8796742 0.0007788 2 0.1728844 0.0078460 CTX Foxg1 Gm10801
Dcun1d1 0.0638298 0.5018005 2.6696390 0.0036561 2 0.8116467 0.0253957 CTX Foxg1 Gm10801
Ccser1.var1 0.1063830 0.4956600 2.1767906 0.0008129 2 0.1804591 0.0078460 CTX Foxg1 Gm10801
mt-Rnr2 0.8819562 0.3448005 0.2047558 0.0000000 0 0.0000000 0.0000000 CTX Foxg1 Mt-rnr2
Trim30a 0.4873524 0.0288394 0.0430229 0.0378094 0 0.7561883 0.3780942 CTX Foxg1 Mt-rnr2


7.5 Heatmap of cell subclasses - log(CPM + 1)

7.6 Heatmap of cell subclasses - scale(log(CPM + 1))




8 Subtypes identification based on CSSG genes

8.1 UMAP visualization


8.2 Subtypes - cell composition


8.3 Subtypes markers - top 25


Top 25 markers
genes pct_occurrence esm avg_logFC p_val subtype p_adj_bf p_adj_bh cluster
Adgrl3 1.0000000 2.1759120 2.2703800 0.0000000 CTX Emx1 Mt-rnr2 - Adgrl3 0.0000000 0.0000000 0
Gm32067 0.6274510 2.4062788 3.8623922 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Dip2b 1.0000000 2.2154857 2.5036859 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Olfr1109 0.4117647 1.8675132 4.0979103 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Marchf1 0.5098039 1.7056346 3.1833069 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Prune2 0.2941176 1.6273738 4.5361811 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Cux2 0.2941176 1.5625361 4.3228766 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Tor3a 0.5294118 1.5181786 2.8672930 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Usp54 0.3725490 1.5081065 3.4820401 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
4931429P17Rik 0.3137255 1.5033152 3.9944412 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
D630023O14Rik 0.1764706 1.4126324 5.9645874 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Onecut2 0.5294118 1.3876064 2.5421324 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Arhgap31 0.3137255 1.3634223 3.5483788 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Rnf19a 0.2941176 1.3562895 3.6327735 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Cdk8 0.5294118 1.3482082 2.4884015 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Gabrd 0.2156863 1.3215989 4.3948169 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Csnk1g1 0.3137255 1.3180396 3.4232340 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Efhd1 0.1764706 1.3050869 5.1644702 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Gm34719 0.1764706 1.2983052 5.1314056 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Cbr3 0.1960784 1.2894168 4.7085943 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
4930556M19Rik 0.1960784 1.2857535 4.7012500 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Gm12679 0.2549020 1.2749375 3.8274563 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Flt3 0.1568627 1.2612213 5.6081273 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Arhgap18 0.2549020 1.2571639 3.7240657 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Sh3yl1 0.3137255 1.2517741 3.2391273 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Trdmt1 0.7843137 1.2356213 1.6695128 0.0000000 CTX Foxg1 Cdh23.var1 - Dip2b 0.0000000 0.0000000 1
Faf1.var1 0.2941176 3.3114895 7.1077690 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Nfib.var1 1.0000000 2.2962135 2.7406478 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Pik3ca 0.1764706 2.2856142 6.2190926 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
B3gnt5 0.1176471 2.1125210 7.3708281 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Degs1 0.1176471 2.1125074 7.2185105 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Gdap1 0.1176471 2.1125074 7.2185105 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Gt(ROSA)26Sor 0.1176471 2.1125074 7.2185105 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Mvd 0.1176471 2.1125074 7.2185105 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Pdss1 0.1176471 2.1125074 7.2185105 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Shisa2 0.1176471 2.1125074 7.2185105 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Zfp408 0.1176471 2.1125074 7.2185105 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Ikbip 0.1176471 2.1124118 7.6612103 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Nmd3 0.1176471 2.1119719 7.2543696 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Scand1 0.1176471 2.1119719 7.2543696 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Tram1l1 0.1176471 2.1119719 7.2543696 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Katnbl1 0.1176471 2.1118822 7.4042283 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Lifr 0.1176471 2.1117856 7.2496474 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Snrnp48 0.1176471 2.1117856 7.2496474 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Umps 0.1176471 2.1117856 7.2496474 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Fancc 0.1176471 2.1114406 7.3284956 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Abcb8 0.1176471 2.1099555 7.4476811 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Gm12350 0.1176471 2.1093709 7.2989000 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Saal1 0.1176471 2.1089459 7.2943215 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Gfm2 0.1176471 2.1060564 7.3330042 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Colgalt1 0.1176471 2.1053257 7.3296478 0.0000000 CTX Foxg1 Cdh23.var1 - Nfib.var1 0.0000000 0.0000000 1
Gm10718 0.9200000 10.3449031 7.3900604 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000000 0.0000000 2
Gm33838 1.0000000 9.1280116 6.2640899 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000000 0.0000000 2
Gm10722 0.8800000 6.7628829 6.0734526 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000000 0.0000000 2
Gm10717 0.7200000 6.1195030 6.9894671 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000000 0.0000000 2
Gm10801 0.9600000 5.2812824 4.8093790 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000000 0.0000000 2
Gm11168 0.4400000 4.2254017 9.6988161 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000000 0.0000000 2
Gm10719 0.5200000 4.0843766 6.4873682 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000000 0.0000000 2
Gm10800 0.9200000 3.9127525 4.0320202 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000000 0.0000000 2
Gm10721 0.3600000 3.3642292 7.4793644 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000000 0.0000000 2
Dnajc1 0.1200000 1.3679911 5.0199700 0.0000000 CTX Foxg1 Gm10801 - Gm33838 0.0000001 0.0000000 2
Grb2 0.1200000 1.0001602 3.7176376 0.0000036 CTX Foxg1 Gm10801 - Gm33838 0.0002037 0.0000185 2
Ints13 0.1200000 0.8543048 3.2304585 0.0000613 CTX Foxg1 Gm10801 - Gm33838 0.0034343 0.0002862 2
Gpm6b 0.1600000 0.6691492 2.1688539 0.0034731 CTX Foxg1 Gm10801 - Gm33838 0.1944955 0.0149612 2
Rufy3 0.1200000 0.6554352 2.4723140 0.0038493 CTX Foxg1 Gm10801 - Gm33838 0.2155588 0.0153971 2
Ttc28.var1 0.1200000 0.6306612 2.3438878 0.0079540 CTX Foxg1 Gm10801 - Gm33838 0.4454260 0.0247459 2
Zfp462 0.1200000 0.6304118 2.3829412 0.0057779 CTX Foxg1 Gm10801 - Gm33838 0.3235650 0.0212900 2
Dmtn 0.1200000 0.6111338 2.2961561 0.0079059 CTX Foxg1 Gm10801 - Gm33838 0.4427307 0.0247459 2
Ccser1.var1 0.1200000 0.5976588 2.3037403 0.0060829 CTX Foxg1 Gm10801 - Gm33838 0.3406403 0.0212900 2
Macf1 0.1200000 0.5797563 2.1947250 0.0121516 CTX Foxg1 Gm10801 - Gm33838 0.6804900 0.0358153 2
Chd4 0.1600000 0.5056084 1.7260832 0.0167051 CTX Foxg1 Gm10801 - Gm33838 0.9354833 0.0466305 2
Cdc42bpa 0.1200000 0.5003598 1.9688777 0.0174864 CTX Foxg1 Gm10801 - Gm33838 0.9792409 0.0466305 2
Large1.var1 0.1200000 0.4405302 1.7196767 0.0437463 CTX Foxg1 Gm10801 - Gm33838 1.0000000 0.1113541 2
Trim30a 1.0000000 2.2325071 1.9633145 0.0000000 CTX Foxg1 Mt-rnr2 - Trim30a 0.0000000 0.0000000 0
Fabp7 0.1628959 0.2948929 1.1627236 0.0009637 CTX Foxg1 Mt-rnr2 - Trim30a 0.0905872 0.0406421 0
Cdk4 0.1176471 0.2741735 1.3221302 0.0021618 CTX Foxg1 Mt-rnr2 - Trim30a 0.2032105 0.0406421 0
Afm 0.1900452 0.2719298 0.9529706 0.0020540 CTX Foxg1 Mt-rnr2 - Trim30a 0.1930730 0.0406421 0
Hnrnpa2b1 0.2624434 0.2716742 0.7547639 0.0019845 CTX Foxg1 Mt-rnr2 - Trim30a 0.1865445 0.0406421 0
Rps2 0.1493213 0.2610742 1.0676691 0.0030773 CTX Foxg1 Mt-rnr2 - Trim30a 0.2892638 0.0482106 0
Atp5pb 0.1040724 0.2591536 1.3376355 0.0038747 CTX Foxg1 Mt-rnr2 - Trim30a 0.3642173 0.0489335 0
Cnbp 0.1085973 0.2517574 1.2601624 0.0041645 CTX Foxg1 Mt-rnr2 - Trim30a 0.3914676 0.0489335 0
Ptma 0.3167421 0.2459208 0.5881911 0.0050507 CTX Foxg1 Mt-rnr2 - Trim30a 0.4747642 0.0527516 0
Hsp90ab1 0.2488688 0.2374417 0.6768330 0.0077140 CTX Foxg1 Mt-rnr2 - Trim30a 0.7251153 0.0725115 0
Foxg1 0.1176471 0.2315929 1.0639234 0.0107295 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.0840481 0
Rplp0 0.1583710 0.2263801 0.8707091 0.0088856 CTX Foxg1 Mt-rnr2 - Trim30a 0.8352508 0.0759319 0
Rps15a 0.1312217 0.2245464 0.9671396 0.0119566 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.0859406 0
Rpl19 0.1085973 0.2191339 1.0573490 0.0157673 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.0988085 0
mt-Nd2 0.1855204 0.2180027 0.7482510 0.0127997 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.0859406 0
Rpl18a 0.2036199 0.2055220 0.6555629 0.0200491 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1108908 0
H2az1 0.1131222 0.2033407 0.9456098 0.0224556 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1108908 0
Grm8.var1 0.1900452 0.2030050 0.6737175 0.0220805 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1108908 0
Tuba1a 0.3574661 0.2029167 0.4331069 0.0235938 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1108908 0
Rpsa 0.1855204 0.2001264 0.6732538 0.0233572 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1108908 0
Eef1a1 0.2262443 0.1961794 0.5787683 0.0296120 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1185075 0
Tlk1 0.1176471 0.1945612 0.8755234 0.0257185 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1151207 0
Rps21 0.1176471 0.1922929 0.8663250 0.0328908 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1185075 0
Pkm 0.1085973 0.1915755 0.9028033 0.0332047 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1185075 0
Rpl7 0.1628959 0.1894044 0.6976822 0.0293199 CTX Foxg1 Mt-rnr2 - Trim30a 1.0000000 0.1185075 0
Psmc2 1.0000000 2.3943113 2.5631470 0.0000000 CTX Tbr1 Mt-rnr2 - Psmc2 0.0000000 0.0000000 0
Tmeff1 0.1111111 0.9591044 3.8229860 0.0000017 CTX Tbr1 Mt-rnr2 - Psmc2 0.0000576 0.0000288 0
Casp3 0.1111111 0.6713362 2.7744410 0.0002352 CTX Tbr1 Mt-rnr2 - Psmc2 0.0079975 0.0026658 0
Crmp1 0.1111111 0.5032146 2.0116047 0.0117167 CTX Tbr1 Mt-rnr2 - Psmc2 0.3983689 0.0995922 0
Fbxo17 0.1111111 0.3988742 1.6290507 0.0351709 CTX Tbr1 Mt-rnr2 - Psmc2 1.0000000 0.1993017 0
Cdh23.var1 0.8888889 0.2968211 0.2084660 0.0250235 CTX Tbr1 Mt-rnr2 - Psmc2 0.8507984 0.1701597 0
Actb 1.0000000 2.7367861 2.8337028 0.0000000 HIP Lhx2 Mt-rnr2 - Actb 0.0000000 0.0000000 0
Gm35769 0.2666667 0.8998376 2.4290080 0.0000000 HIP Lhx2 Mt-rnr2 - Actb 0.0000001 0.0000000 0
Calu 0.1166667 0.6764668 3.0351923 0.0000011 HIP Lhx2 Mt-rnr2 - Actb 0.0000710 0.0000237 0
Rpl28 0.2000000 0.6520709 2.0697418 0.0000076 HIP Lhx2 Mt-rnr2 - Actb 0.0004728 0.0001182 0
Ndufa4 0.1333333 0.5425358 2.2237514 0.0000640 HIP Lhx2 Mt-rnr2 - Actb 0.0039667 0.0007933 0
Slc25a4 0.1666667 0.3908672 1.3349424 0.0069692 HIP Lhx2 Mt-rnr2 - Actb 0.4320883 0.0720147 0
Trir 0.1166667 0.3446610 1.4415171 0.0179158 HIP Lhx2 Mt-rnr2 - Actb 1.0000000 0.1586831 0
Map1b 0.1833333 0.2887209 0.9237075 0.0450162 HIP Lhx2 Mt-rnr2 - Actb 1.0000000 0.3214989 0
H3f3a 0.2000000 0.2767060 0.8488499 0.0466692 HIP Lhx2 Mt-rnr2 - Actb 1.0000000 0.3214989 0
Cracd 1.0000000 4.3413964 4.1335799 0.0000000 HIP Lhx2 Mt-rnr2 - Cracd 0.0000000 0.0000000 0
Tox4 0.1428571 1.4968645 4.5800441 0.0000001 HIP Lhx2 Mt-rnr2 - Cracd 0.0000060 0.0000030 0
Mgat5b 0.1428571 1.3409596 4.0688387 0.0000064 HIP Lhx2 Mt-rnr2 - Cracd 0.0006948 0.0001507 0
Prdx5 0.1428571 1.3278173 4.0581379 0.0000069 HIP Lhx2 Mt-rnr2 - Cracd 0.0007534 0.0001507 0
Fat4 0.1428571 1.2843780 3.9871693 0.0000066 HIP Lhx2 Mt-rnr2 - Cracd 0.0007235 0.0001507 0
Cotl1 0.1428571 1.2492148 3.8385490 0.0000316 HIP Lhx2 Mt-rnr2 - Cracd 0.0034487 0.0005748 0
Rpl13 0.3571429 1.1645345 2.4332021 0.0000435 HIP Lhx2 Mt-rnr2 - Cracd 0.0047409 0.0006773 0
Sh3bp5 0.1428571 1.1530322 3.5200547 0.0002418 HIP Lhx2 Mt-rnr2 - Cracd 0.0263534 0.0027486 0
Dtnb 0.4285714 1.0976542 2.1132699 0.0000653 HIP Lhx2 Mt-rnr2 - Cracd 0.0071185 0.0008898 0
Eef1g 0.2857143 1.0718869 2.4659255 0.0002805 HIP Lhx2 Mt-rnr2 - Cracd 0.0305781 0.0027486 0
Gm4366 0.1428571 1.0697561 3.3255728 0.0005367 HIP Lhx2 Mt-rnr2 - Cracd 0.0585000 0.0045000 0
Snx10 0.1428571 1.0530481 3.3737997 0.0002902 HIP Lhx2 Mt-rnr2 - Cracd 0.0316315 0.0027486 0
St18 0.1428571 1.0515638 3.3733466 0.0003026 HIP Lhx2 Mt-rnr2 - Cracd 0.0329829 0.0027486 0
Hsd17b12 0.1428571 0.9801404 3.1303315 0.0011759 HIP Lhx2 Mt-rnr2 - Cracd 0.1281701 0.0085447 0
Pitpnb 0.1428571 0.9604932 3.0931674 0.0011489 HIP Lhx2 Mt-rnr2 - Cracd 0.1252307 0.0085447 0
Psme3 0.1428571 0.9405393 3.0119448 0.0020125 HIP Lhx2 Mt-rnr2 - Cracd 0.2193584 0.0121866 0
Smc1a 0.1428571 0.9337071 2.9489503 0.0031978 HIP Lhx2 Mt-rnr2 - Cracd 0.3485556 0.0183450 0
Wnk1 0.1428571 0.9139764 2.9649732 0.0019699 HIP Lhx2 Mt-rnr2 - Cracd 0.2147177 0.0121866 0
Mllt3 0.2142857 0.8616247 2.4110290 0.0020014 HIP Lhx2 Mt-rnr2 - Cracd 0.2181518 0.0121866 0
Ncoa1 0.1428571 0.8613500 2.7505360 0.0071277 HIP Lhx2 Mt-rnr2 - Cracd 0.7769245 0.0356196 0
Ndufa6 0.1428571 0.8301252 2.7769354 0.0038164 HIP Lhx2 Mt-rnr2 - Cracd 0.4159836 0.0207992 0
Elavl3 0.1428571 0.7970417 2.6283762 0.0071893 HIP Lhx2 Mt-rnr2 - Cracd 0.7836318 0.0356196 0
Epha4 0.1428571 0.7849074 2.5750942 0.0101405 HIP Lhx2 Mt-rnr2 - Cracd 1.0000000 0.0442126 0
Eif1ax 0.1428571 0.7673469 2.5389928 0.0098189 HIP Lhx2 Mt-rnr2 - Cracd 1.0000000 0.0442126 0
Rpl7-ps7 0.1428571 0.7481943 2.5108011 0.0109859 HIP Lhx2 Mt-rnr2 - Cracd 1.0000000 0.0450627 0
Zfp263 1.0000000 2.4900947 2.6600593 0.0000000 HIP Lhx2 Mt-rnr2 - Zfp263 0.0000000 0.0000000 0
Gnai3 0.1041667 0.5885046 2.5767424 0.0003847 HIP Lhx2 Mt-rnr2 - Zfp263 0.0192342 0.0064114 0
Gm15500 0.1458333 0.5766988 2.1370966 0.0002662 HIP Lhx2 Mt-rnr2 - Zfp263 0.0133100 0.0064114 0
Pcgf5 0.1458333 0.4378360 1.5770827 0.0076492 HIP Lhx2 Mt-rnr2 - Zfp263 0.3824615 0.0956154 0
Rpl5-ps1 0.1041667 0.4010093 1.7544370 0.0125557 HIP Lhx2 Mt-rnr2 - Zfp263 0.6277859 0.1255572 0
Cse1l 0.1041667 0.3837506 1.6259381 0.0260587 HIP Lhx2 Mt-rnr2 - Zfp263 1.0000000 0.1924005 0
Grtp1 0.1041667 0.3784897 1.6101445 0.0269361 HIP Lhx2 Mt-rnr2 - Zfp263 1.0000000 0.1924005 0
Trpc4 0.1458333 0.3288938 1.1717066 0.0429275 HIP Lhx2 Mt-rnr2 - Zfp263 1.0000000 0.2384863 0
mt-Rnr2 0.8750000 0.1029803 0.0581472 0.0414073 HIP Lhx2 Mt-rnr2 - Zfp263 1.0000000 0.2384863 0
Cdh13.var1 1.0000000 3.6957805 3.7254609 0.0000000 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0000000 0.0000000 0
Sphk2 0.1666667 3.0794291 8.3593756 0.0000000 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0000000 0.0000000 0
Stard9 0.1666667 3.0765997 8.3426832 0.0000000 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0000000 0.0000000 0
Fbp2 0.1666667 2.3024650 6.0459530 0.0000000 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0000000 0.0000000 0
Hsd17b4 0.2500000 1.9064409 4.2189546 0.0000000 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0000002 0.0000000 0
Cdk14 0.1666667 1.7239751 4.5941767 0.0000001 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0000047 0.0000007 0
Ank2.var1 0.2500000 1.7150628 3.9661696 0.0000000 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0000014 0.0000002 0
Serinc3 0.1666667 1.5175461 4.2132863 0.0000009 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0000574 0.0000067 0
Zfp428 0.1666667 1.4901004 4.1769103 0.0000009 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0000602 0.0000067 0
Lrrc4c 0.1666667 1.4416775 4.0195542 0.0000048 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0003069 0.0000307 0
Macroh2a2 0.1666667 1.4391829 3.9179379 0.0000191 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0012243 0.0001113 0
Gbf1 0.1666667 1.2496869 3.5934047 0.0000582 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0037230 0.0003103 0
Gdpd1 0.1666667 1.2373176 3.5147601 0.0001541 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0098609 0.0007585 0
Erh 0.1666667 1.1045866 3.2160514 0.0006449 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0412723 0.0027515 0
Kansl1 0.1666667 1.0874738 3.2440992 0.0003576 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0228865 0.0016348 0
Snrpg 0.1666667 1.0624357 3.0985526 0.0009991 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0639401 0.0037612 0
Top1 0.3333333 1.0466885 2.2428058 0.0007492 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0479482 0.0029968 0
Mycn 0.1666667 1.0080408 3.0194711 0.0010843 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.0693956 0.0038553 0
6030443J06Rik 0.1666667 0.9580883 2.9033824 0.0020708 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.1325327 0.0064477 0
Midn 0.1666667 0.9494962 2.8900923 0.0019001 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.1216075 0.0064004 0
Atp5o.var2 0.1666667 0.9377545 2.7900429 0.0039749 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.2543955 0.0110607 0
Psmd13 0.1666667 0.9369532 2.8782068 0.0022555 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.1443514 0.0065614 0
Tcerg1 0.1666667 0.8915705 2.8001041 0.0021156 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.1354011 0.0064477 0
Mllt11 0.1666667 0.8743143 2.6545727 0.0054677 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.3499320 0.0145805 0
Id2 0.1666667 0.8251033 2.4787674 0.0127966 STR Foxp1 Mt-rnr2 - Cdh13.var1 0.8189822 0.0327593 0
Dynll2 1.0000000 6.2715042 5.1554995 0.0000000 STR Foxp1 Mt-rnr2 - Dynll2 0.0000000 0.0000000 0
Gm6540 0.1538462 2.8194794 8.2402049 0.0000000 STR Foxp1 Mt-rnr2 - Dynll2 0.0000000 0.0000000 0
Ccnd2 0.6153846 2.3188025 3.2267531 0.0000000 STR Foxp1 Mt-rnr2 - Dynll2 0.0000000 0.0000000 0
Impdh2 0.1538462 1.8060374 5.1547612 0.0000000 STR Foxp1 Mt-rnr2 - Dynll2 0.0000000 0.0000000 0
Wipi1 0.1538462 1.6317788 4.4023342 0.0000023 STR Foxp1 Mt-rnr2 - Dynll2 0.0002393 0.0000356 0
Ndel1 0.1538462 1.4778308 4.2034406 0.0000023 STR Foxp1 Mt-rnr2 - Dynll2 0.0002393 0.0000356 0
Pqbp1 0.1538462 1.4612217 4.1836529 0.0000025 STR Foxp1 Mt-rnr2 - Dynll2 0.0002613 0.0000356 0
Setd2 0.1538462 1.3528421 4.0494816 0.0000027 STR Foxp1 Mt-rnr2 - Dynll2 0.0002852 0.0000356 0
Gm13456 0.1538462 1.3212397 3.8023041 0.0000429 STR Foxp1 Mt-rnr2 - Dynll2 0.0045512 0.0004199 0
Cdc123 0.1538462 1.2610491 3.7182546 0.0000460 STR Foxp1 Mt-rnr2 - Dynll2 0.0048708 0.0004199 0
Cyb5r3 0.1538462 1.2473821 3.6317722 0.0001251 STR Foxp1 Mt-rnr2 - Dynll2 0.0132605 0.0010066 0
Arhgap11a 0.1538462 1.2375468 3.6935636 0.0000475 STR Foxp1 Mt-rnr2 - Dynll2 0.0050385 0.0004199 0
Cenpb 0.1538462 1.2097038 3.5748355 0.0001329 STR Foxp1 Mt-rnr2 - Dynll2 0.0140919 0.0010066 0
Dars 0.1538462 1.1098694 3.3602734 0.0003183 STR Foxp1 Mt-rnr2 - Dynll2 0.0337427 0.0021089 0
Tpt1 0.6153846 1.1056760 1.6863578 0.0000465 STR Foxp1 Mt-rnr2 - Dynll2 0.0049334 0.0004199 0
Ccdc50 0.1538462 1.0916855 3.2771433 0.0006612 STR Foxp1 Mt-rnr2 - Dynll2 0.0700822 0.0031856 0
Pdhb 0.1538462 1.0772720 3.2549052 0.0006448 STR Foxp1 Mt-rnr2 - Dynll2 0.0683459 0.0031856 0
Trappc1 0.1538462 1.0633134 3.2352592 0.0006209 STR Foxp1 Mt-rnr2 - Dynll2 0.0658161 0.0031856 0
Rpl14-ps1 0.1538462 1.0534183 3.2175263 0.0006612 STR Foxp1 Mt-rnr2 - Dynll2 0.0700822 0.0031856 0
Smyd3.var1 0.1538462 1.0517621 3.2765585 0.0003183 STR Foxp1 Mt-rnr2 - Dynll2 0.0337427 0.0021089 0
Senp5 0.1538462 1.0508760 3.1572843 0.0011218 STR Foxp1 Mt-rnr2 - Dynll2 0.1189138 0.0051702 0
Rpl18 0.2307692 1.0255263 2.7079740 0.0004202 STR Foxp1 Mt-rnr2 - Dynll2 0.0445391 0.0026199 0
mt-Co1 0.4615385 1.0062840 1.8883374 0.0004602 STR Foxp1 Mt-rnr2 - Dynll2 0.0487816 0.0027101 0
Tm2d1 0.1538462 0.9925999 3.0164391 0.0018875 STR Foxp1 Mt-rnr2 - Dynll2 0.2000740 0.0083364 0
Mki67 0.1538462 0.9895409 3.0174655 0.0019702 STR Foxp1 Mt-rnr2 - Dynll2 0.2088392 0.0083536 0


8.4 Heatmap of cell subtypes - log(CPM + 1)

8.5 Heatmap of cell subtypes - scale(log(CPM + 1))




9 Disclaimer

The analysis was performed through the non-profit and open-source pipeline JSEQ_scRNAseq. Remember, in silico analysis must be validated in vitro or in vivo. For more information, visit GitHub or contact us. JSEQ_scRNAseq was created at the Institute of Bioorganic Chemistry, Polish Academy of Sciences.